相关论文: Statistical mechanics of columnar DNA assemblies

Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications…

Quantum phase transitions in the two-dimensional Kugel-Khomski model on a square lattice are studied using the plaquette mean field theory and the entanglement renormalization ansatz. When $3z^2-r^2$ orbitals are favored by the crystal…

Evidence of a special chiral nematic phase is provided using numerical simulation and Onsager theory for systems of hard helical particles. This phase appears at the high density end of the nematic phase, when helices are well aligned, and…

Magnetic textures are promising candidates for unconventional computing due to their non-linear dynamics. We propose to investigate the rich variety of seemingly trivial lamellar magnetic phases, e.g., helical, spiral, stripy phase, or…

Peaks in the probabilities of loops or bubbles, helical segments, and unzipping ends in melting DNA are found in this article using a peak finding method that maps the hierarchical structure of certain energy landscapes. The peaks indicate…

We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…

We test the performance of a recently proposed fundamental measure density functional of aligned hard cylinders by calculating the phase diagram of a monodisperse fluid of these particles. We consider all possible liquid crystalline…

The macroscopic curvature of double helical DNA induced by regularly repeated adenine tracts is well-known but still puzzling. Its physical origin remains controversial even though it is perhaps the best-documented sequence modulation of…

This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…

In this article, I have investigated statistical mechanics of a non-stretched elastica in two dimensional space using path integral method. In the calculation, the MKdV hierarchy naturally appeared as the equations including the temperature…

The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) plays an exceptional role in structural studies of DNA because this effect presents the most well-documented example of sequence…

We consider an elastic rod model for twisted DNA in the plectonemic regime. The molecule is treated as an impenetrable tube with an effective, adjustable radius. The model is solved analytically and we derive formulas for the contact…

It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…

We study the Kondo lattice Shastry-Sutherland model with additional Dzyaloshinskii-Moriya(DM) interactions, exploring the possible magnetic phases in its multi-dimensional parameter space. Treating the local moments as classical spins and…

The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) is a long known, but still unexplained phenomenon. This effect plays a key role in DNA studies because it is unique in the amount…

The experiment that the high spin selectivity and the length-dependent spin polarization are observed in double-stranded DNA [Science ${\bf 331}$, 894 (2011)], is elucidated by considering the combination of the spin-orbit coupling, the…

It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…

We report on our theoretical investigations of the electronic states in a DNA molecule. We have used a two-leg charge ladder model where electron-electron interactions and the electron spin have been taken into account. The energy spectra…

It now becomes apparent that condensed DNA toroid which emerges in a poor solvent condition can be realised in the framework of the non-linear sigma model on a line segment. In fact, the classical solutions of the model, i.e., of the…

The Yakushevich (Y) model provides a very simple pictures of DNA torsion dynamics, yet yields remarkably correct predictions on certain physical characteristics of the dynamics. In the standard Y model, the interaction between bases of a…